Covid sequencing is a critical and quickly emerging technology for diagnosing COVID-19 and for understanding its dissemination and management.
A genome is defined as the genetic material of an organism that is effectively its instruction manual, including all the information necessary to build and sustain it. Genomes of humans are being constructed from double-stranded DNA and are encoded using a unique code consisting of four nucleotide base ‘letters’ and this human genome has about 3 billion base letters. In comparison, a viral genome is made up of either DNA or its near relative RNA and is extremely small. Because coronaviruses are classified as RNA viruses, the SARS-CoV-2 virus that has been recently discovered comprises a single short RNA strand that is only 30,000 letters in length and using a process called sequencing, these letters may be read one by one.
Genomes are used to classify viruses
If the novel coronavirus sequence is discovered in a sample (often from the nose or mouth), it confirms that a patient’s symptoms are consistent with COVID-19.
Virus genomes are continually mutating by modifying a few letters at a time as they split and spread through infection, but with sequencing, documenting, and analyzing genomes, these alterations may be used to monitor the virus’s transmission.
If virus genome sequencing is carried out fast and on a wide scale, it can aid epidemiologists and public health officials in determining how the virus spreads and evaluating the effectiveness of their treatments. Additionally, it can aid in determining if novel variations are connected with certain symptom patterns or illness severity. In the longer run, tracking new variations is expected to be critical to ensuring that vaccinations created in the future remain up to date with the virus strains presently circulating.
Transmission within the community versus imported cases
During the early phases of an epidemic, sequencing may be employed to determine how many new instances of illness are imported or transmitted locally.
Global viral genome databases help scientists to compare genomes in order to get an accurate estimate of local transmission in each country.
Growth of an epidemic
Mathematical models of virus evolution during an epidemic have been developed through extensive analysis of previous outbreaks thereby enabling the estimation of epidemic growth rates as well as other measures of transmission including infection from virus genome sequences. In comparison to other data sources, insights from viral genetics are more valuable for forecasting longer-term, larger-scale changes. Notably, they enable independent confirmation of estimates of an epidemic’s magnitude and growth rate. This is particularly useful when cases are under-reported, as many people who are infected do not exhibit symptoms.
Dispersed in several locations or groupings
The widespread sampling, as well as genome sequencing of the novel coronavirus, enables the reconstruction of the virus’s dissemination in diverse locations or populations. This gives insight into the factors that contribute to the virus’s transmission not just locally but nationally. This work may be enhanced by combining viral genomes with data on where, how, and when individuals move locally and globally.
Chains of transmission
Additionally, viral genome sequences can reveal unique genetic modifications shared by all infected individuals in a particular virus transmission chain. This may be used to determine if two clusters of cases in the same location occurred as a result of infection spreading from one to the other, or as a result of two unique as well as independent channels of transmission with distinct, earlier beginnings. Thus, data can now be supplemented with the use of virus genomes that are being collected through contract tracing of patients, which is essential in tracking epidemics in communities, hospitals, and other care settings.
Variation in genetic material
Numerous genetic alterations in the virus’s genome have no discernible influence on the course of infection or sickness, or on the effectiveness of control efforts. But, there are some modifications that may be essential and these must be recognized and followed over time. We know that genetic alterations in viruses such as influenza, for example, can affect how the immune system recognizes viruses, antiviral medication resistance, and illness severity and these discoveries have not yet been made regarding the newly discovered coronavirus.
Rapid, large-scale viral genome sequencing generates a fresh stream of data that may be used to follow epidemics and create novel control measures. Its application to the newly discovered coronavirus is barely getting started.
How critical is genetic sequencing to the response to COVID-19?
Genomic sequencing played a critical role in the COVID-19 response. As new variations emerge on a daily basis, genomic data has aided governments in making timely and informed public health choices since the epidemic began. For instance, we notified our Ministry of Health and President Cyril Ramaphosa promptly upon discovering the Beta variety in South Africa very soon in our second wave. In less than a day, new laws were prepared to place the country on a higher degree of lockdown in order to prevent infection and preserve lives. That took just under 48 hours after learning about the new variety. and the Delta variation in the third wave was the same.
The relevance of genetic sequencing for public health response extends beyond just determining when to implement lockdown procedures. It can assist counties in preparing for future surges and taking critical actions such as increasing oxygen supply, expanding hospital beds, and ramping up testing since these are more transmissible varieties. Additionally, it was critical to assist governments in identifying the most suitable vaccines for use in Africa. Vaccine hesitancy is a significant issue, and we must do it right the first time and guarantee that the vaccines implemented are the most effective possible. South Africa’s choice to utilize Johnson & Johnson and Pfizer COVID-19 vaccinations were based on genomic data.
Additionally, governments can take efforts to respond to novel variations without access to their genetic data. Angola is an excellent illustration of how modest public health measures may effectively prevent variations from entering the country. The government has isolated the majority of positive cases and reduced the transmission of these more deadly varieties of concern without implementing a travel restriction. Economically, travel restrictions are too expensive, but a competent triage system and screening at the point of entry are virtually as effective. I believe that the world may benefit significantly from this plan and from Dr. Silvia Lutucuta, Angola’s Minister of Health, and Dr. Joana Moraes, Angola’s Director-General of Health.